communicability: Compute Communicability between Nodes in an HBM
In hbm: Hierarchical Block Matrix Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/hbm.R

communicability computes the scale communicability between nodes (rows) in a hierarchical block matrix hm, generated with hbm.

1	communicability(hm)

`hm`	a hierarchical block matrix computed with `hbm`, with: hm_{i,j} = the minimal scale (iteration) at which i and j were clustered together, or 0 if i=j

The communicability of an adjacency matrix A can be expressed as e^A (Estrada et al., 2012), so that the i,j-th entry is a weighted sum of all paths from i to j, where shortest paths are assigned with larger weights. For a hierarchical block matrix, computed with hbm, each scale s defines its own adjacency matrix, where all entries with values larger than s are set to 0. The scale-communicability between 2 nodes i and j in this matrix is defined here as the mean communicability across scales (excluding the largest scale).

communicability returns a matrix of the same dimensions as hm, where the (i,j)-th entry gives the scale-communicability between i and j in hm.

Yoli Shavit

Estrada, E., Hatano, N. and Benzi, M. The physics of communicability in complex networks. Physics Reports 514, 89-119 (2012).

hbm's website: http://www.cl.cam.ac.uk/~ys388/hbm/

hbm to learn how to build hierarchical block matrices
hbm's tutorials at http://www.cl.cam.ac.uk/~ys388/hbm/

set.seed(2)
n = 100 # chain size
conf = generate.random.conf(n, scale = FALSE)

# compute the HBM
hm.control = hbm(exp(-1*as.matrix(dist(conf))), 2)$hm

# compute scale communicability
comm = communicability(hm.control)

# explore for position 50
plot(1:n, comm[50,], xlab = "Position", ylab = "Communicability", 
main = "Communicability for Position 50", pch=16)

# plot in original configuration
cols = rep("black", n)
cols[which(comm[50,] > 100)] = "blue"
plot(conf, xlab = "X", ylab = "Y", type = "n")
text(conf, labels = 1:n, col = cols)